Arrupe studied medicine at the University of Madrid, but, after witnessing the poverty in that city, he left school to join the Jesuits in 1927. When the Spanish government dissolved the Jesuit order in Spain in 1932, Arrupe continued his religious studies elsewhere in Europe and in the United States, where he was ordained at St. Mary’s Seminary in Kansas in 1936. In 1938 he went to Japan, where he took his final vows as a Jesuit in 1943 and spent a total of 27 years as a missionary. In 1945 he headed the first rescue party to go into Hiroshima after that city had been devastated by the atomic bomb. He subsequently became Jesuit vice provincial (1954–58) and then the first Jesuit provincial for Japan (1958–65).

Arrupe was elected superior general of the Jesuits in 1965. He led the Society of Jesus during an upsurge of liberalism among some of its members, who supported such ideas as a married priesthood and social and political work among the poor in developing countries(i. e., liberation theology). In the 1970s these activities brought the Jesuits into conflict with the papacy, which Pope John Paul II, who regarded the moderately liberal Arrupe as being overly permissive in his administration of the order. Arrupe resigned in 1983 owing to ill health and was in fact the first Jesuit superior general to resign instead of remaining in office until his death.